Examples with ValuePair net.imglib2.util.ValuePair used on opensource projects

Example 1 with ValuePair

use of net.imglib2.util.ValuePair in project imagej-ops by imagej.

the class DefaultConvexHull3D method computeMinMax.

/**
 * Finds for each dimension the min and max vertex.
 *
 * @return min and max vertices of each dimension
 */
private Pair<Double, Vertex[]> computeMinMax(final Set<Vertex> vertices) {
    Vertex[] minMax = new Vertex[6];
    double maxX, maxY, maxZ;
    double minX, minY, minZ;
    Iterator<Vertex> it = vertices.iterator();
    Vertex initPoint = it.next();
    for (int i = 0; i < minMax.length; i++) {
        minMax[i] = initPoint;
    }
    minX = maxX = initPoint.getX();
    minY = maxY = initPoint.getY();
    minZ = maxZ = initPoint.getZ();
    while (it.hasNext()) {
        Vertex v = it.next();
        if (v.getX() > maxX) {
            maxX = v.getX();
            minMax[3] = v;
        } else if (v.getX() < minX) {
            minX = v.getX();
            minMax[0] = v;
        }
        if (v.getY() > maxY) {
            maxY = v.getY();
            minMax[4] = v;
        } else if (v.getY() < minY) {
            minY = v.getY();
            minMax[2] = v;
        }
        if (v.getZ() > maxZ) {
            maxZ = v.getZ();
            minMax[5] = v;
        } else if (v.getZ() < minZ) {
            minZ = v.getZ();
            minMax[3] = v;
        }
    }
    // This epsilon formula comes from John Lloyd's quickhull
    // implementation http://www.cs.ubc.ca/~lloyd/java/quickhull3d.html
    final double epsilon = 3 * DOUBLE_PREC * (Math.max(Math.abs(maxX), Math.abs(minX)) + Math.max(Math.abs(maxY), Math.abs(minY)) + Math.max(Math.abs(maxZ), Math.abs(minZ)));
    return new ValuePair<>(epsilon, minMax);
}

Example 2 with ValuePair

use of net.imglib2.util.ValuePair in project imagej-ops by imagej.

the class DefaultMinorMajorAxis method calculate.

@Override
public Pair<DoubleType, DoubleType> calculate(final Polygon2D input) {
    List<RealLocalizable> points = new ArrayList<>(GeomUtils.vertices(input));
    // Sort RealLocalizables of P by x-coordinate (in case of a tie,
    // sort by
    // y-coordinate). Sorting is counter clockwise.
    Collections.sort(points, new Comparator<RealLocalizable>() {

        @Override
        public int compare(final RealLocalizable o1, final RealLocalizable o2) {
            final Double o1x = new Double(o1.getDoublePosition(0));
            final Double o2x = new Double(o2.getDoublePosition(0));
            final int result = o2x.compareTo(o1x);
            if (result == 0) {
                return new Double(o2.getDoublePosition(1)).compareTo(new Double(o1.getDoublePosition(1)));
            }
            return result;
        }
    });
    points.add(points.get(0));
    // calculate minor and major axis
    double[] minorMajorAxis = getMinorMajorAxis(input, points);
    return new ValuePair<>(new DoubleType(minorMajorAxis[0]), new DoubleType(minorMajorAxis[1]));
}

Example 3 with ValuePair

use of net.imglib2.util.ValuePair in project imagej-ops by imagej.

the class DefaultMaximumFeret method calculate.

@Override
public Pair<RealLocalizable, RealLocalizable> calculate(Polygon2D input) {
    final List<? extends RealLocalizable> points = GeomUtils.vertices(function.calculate(input));
    double distance = Double.NEGATIVE_INFINITY;
    RealLocalizable p0 = points.get(0);
    RealLocalizable p1 = points.get(0);
    for (int i = 0; i < points.size(); i++) {
        for (int j = i + 2; j < points.size(); j++) {
            final RealLocalizable tmpP0 = points.get(i);
            final RealLocalizable tmpP1 = points.get(j);
            final double tmp = Math.sqrt(Math.pow(tmpP0.getDoublePosition(0) - tmpP1.getDoublePosition(0), 2) + Math.pow(tmpP0.getDoublePosition(1) - tmpP1.getDoublePosition(1), 2));
            if (tmp > distance) {
                distance = tmp;
                p0 = tmpP0;
                p1 = tmpP1;
            }
        }
    }
    return new ValuePair<>(p0, p1);
}

Example 4 with ValuePair

use of net.imglib2.util.ValuePair in project imagej-ops by imagej.

the class BoxCount method calculate.

/**
 * Counts the number of foreground sections in the interval repeatedly with
 * different size sections
 *
 * @param input an n-dimensional binary interval
 * @return A list of (log(foreground count), -log(section size))
 *         {@link ValuePair} objects for curve fitting
 */
@Override
public List<ValuePair<DoubleType, DoubleType>> calculate(final RandomAccessibleInterval<B> input) {
    final List<ValuePair<DoubleType, DoubleType>> points = new ArrayList<>();
    final int dimensions = input.numDimensions();
    final long[] sizes = new long[dimensions];
    final long numTranslations = 1 + gridMoves;
    input.dimensions(sizes);
    for (long sectionSize = maxSize; sectionSize >= minSize; sectionSize /= scaling) {
        final long translationAmount = Math.max(1, sectionSize / numTranslations);
        final Stream<long[]> translations = translationStream(numTranslations, translationAmount, dimensions - 1, new long[dimensions]);
        final LongStream foregroundCounts = countTranslatedGrids(input, translations, sizes, sectionSize);
        final long foreground = foregroundCounts.min().orElse(0);
        final double logSize = -Math.log(sectionSize);
        final double logCount = Math.log(foreground);
        final ValuePair<DoubleType, DoubleType> point = new ValuePair<>(new DoubleType(logSize), new DoubleType(logCount));
        points.add(point);
    }
    return points;
}

Example 5 with ValuePair

use of net.imglib2.util.ValuePair in project TrakEM2 by trakem2.

the class MatchIntensities method run.

/**
 * @param layers
 * @param radius
 * @param scale
 * @param numCoefficients
 * @param lambda1
 * @param lambda2
 * @param neighborWeight
 * @param roi
 */
public <M extends Model<M> & Affine1D<M>> void run(final List<Layer> layers, final int radius, final double scale, final int numCoefficients, final double lambda1, final double lambda2, final double neighborWeight, final Rectangle roi) throws InterruptedException, ExecutionException {
    final int firstLayerIndex = layerset.getLayerIndex(layers.get(0).getId());
    final int lastLayerIndex = layerset.getLayerIndex(layers.get(layers.size() - 1).getId());
    // final PointMatchFilter filter = new RansacRegressionFilter();
    final PointMatchFilter filter = new RansacRegressionReduceFilter();
    /* collect patches */
    Utils.log("Collecting patches ... ");
    final ArrayList<Patch> patches = new ArrayList<Patch>();
    for (final Layer layer : layers) patches.addAll((Collection) layer.getDisplayables(Patch.class, roi));
    /* delete existing intensity coefficients */
    Utils.log("Clearing existing intensity maps ... ");
    for (final Patch p : patches) p.clearIntensityMap();
    /* generate coefficient tiles for all patches
		 * TODO consider offering alternative models */
    final HashMap<Patch, ArrayList<Tile<? extends M>>> coefficientsTiles = (HashMap) generateCoefficientsTiles(patches, new InterpolatedAffineModel1D<InterpolatedAffineModel1D<AffineModel1D, TranslationModel1D>, IdentityModel>(new InterpolatedAffineModel1D<AffineModel1D, TranslationModel1D>(new AffineModel1D(), new TranslationModel1D(), lambda1), new IdentityModel(), lambda2), numCoefficients * numCoefficients);
    /* completed patches */
    final HashSet<Patch> completedPatches = new HashSet<Patch>();
    /* collect patch pairs */
    Utils.log("Collecting patch pairs ... ");
    final ArrayList<ValuePair<Patch, Patch>> patchPairs = new ArrayList<ValuePair<Patch, Patch>>();
    for (final Patch p1 : patches) {
        completedPatches.add(p1);
        final Rectangle box1 = p1.getBoundingBox().intersection(roi);
        final ArrayList<Patch> p2s = new ArrayList<Patch>();
        /* across adjacent layers */
        final int layerIndex = layerset.getLayerIndex(p1.getLayer().getId());
        for (int i = Math.max(firstLayerIndex, layerIndex - radius); i <= Math.min(lastLayerIndex, layerIndex + radius); ++i) {
            final Layer layer = layerset.getLayer(i);
            if (layer != null)
                p2s.addAll((Collection) layer.getDisplayables(Patch.class, box1));
        }
        for (final Patch p2 : p2s) {
            /*
				 * if this patch had been processed earlier, all matches are
				 * already in
				 */
            if (completedPatches.contains(p2))
                continue;
            patchPairs.add(new ValuePair<Patch, Patch>(p1, p2));
        }
    }
    final int numThreads = Integer.parseInt(layerset.getProperty("n_mipmap_threads", Integer.toString(Runtime.getRuntime().availableProcessors())));
    Utils.log("Matching intensities using " + numThreads + " threads ... ");
    final ExecutorService exec = Executors.newFixedThreadPool(numThreads);
    final ArrayList<Future<?>> futures = new ArrayList<Future<?>>();
    for (final ValuePair<Patch, Patch> patchPair : patchPairs) {
        futures.add(exec.submit(new Matcher(roi, patchPair, (HashMap) coefficientsTiles, filter, scale, numCoefficients)));
    }
    for (final Future<?> future : futures) future.get();
    /* connect tiles within patches */
    Utils.log("Connecting coefficient tiles in the same patch  ... ");
    for (final Patch p1 : completedPatches) {
        /* get the coefficient tiles */
        final ArrayList<Tile<? extends M>> p1CoefficientsTiles = coefficientsTiles.get(p1);
        for (int y = 1; y < numCoefficients; ++y) {
            final int yr = numCoefficients * y;
            final int yr1 = yr - numCoefficients;
            for (int x = 0; x < numCoefficients; ++x) {
                identityConnect(p1CoefficientsTiles.get(yr1 + x), p1CoefficientsTiles.get(yr + x), neighborWeight);
            }
        }
        for (int y = 0; y < numCoefficients; ++y) {
            final int yr = numCoefficients * y;
            for (int x = 1; x < numCoefficients; ++x) {
                final int yrx = yr + x;
                identityConnect(p1CoefficientsTiles.get(yrx), p1CoefficientsTiles.get(yrx - 1), neighborWeight);
            }
        }
    }
    /* optimize */
    Utils.log("Optimizing ... ");
    final TileConfiguration tc = new TileConfiguration();
    for (final ArrayList<Tile<? extends M>> coefficients : coefficientsTiles.values()) {
        // for ( final Tile< ? > t : coefficients )
        // if ( t.getMatches().size() == 0 )
        // IJ.log( "bang" );
        tc.addTiles(coefficients);
    }
    try {
        tc.optimize(0.01f, iterations, iterations, 0.75f);
    } catch (final NotEnoughDataPointsException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (final IllDefinedDataPointsException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    /* save coefficients */
    final double[] ab = new double[2];
    final FSLoader loader = (FSLoader) layerset.getProject().getLoader();
    final String itsDir = loader.getUNUIdFolder() + "trakem2.its/";
    for (final Entry<Patch, ArrayList<Tile<? extends M>>> entry : coefficientsTiles.entrySet()) {
        final FloatProcessor as = new FloatProcessor(numCoefficients, numCoefficients);
        final FloatProcessor bs = new FloatProcessor(numCoefficients, numCoefficients);
        final Patch p = entry.getKey();
        final double min = p.getMin();
        final double max = p.getMax();
        final ArrayList<Tile<? extends M>> tiles = entry.getValue();
        for (int i = 0; i < numCoefficients * numCoefficients; ++i) {
            final Tile<? extends M> t = tiles.get(i);
            final Affine1D<?> affine = t.getModel();
            affine.toArray(ab);
            /* coefficients mapping into existing [min, max] */
            as.setf(i, (float) ab[0]);
            bs.setf(i, (float) ((max - min) * ab[1] + min - ab[0] * min));
        }
        final ImageStack coefficientsStack = new ImageStack(numCoefficients, numCoefficients);
        coefficientsStack.addSlice(as);
        coefficientsStack.addSlice(bs);
        final String itsPath = itsDir + FSLoader.createIdPath(Long.toString(p.getId()), "it", ".tif");
        new File(itsPath).getParentFile().mkdirs();
        IJ.saveAs(new ImagePlus("", coefficientsStack), "tif", itsPath);
    }
    /* update mipmaps */
    for (final Patch p : patches) p.getProject().getLoader().decacheImagePlus(p.getId());
    final ArrayList<Future<Boolean>> mipmapFutures = new ArrayList<Future<Boolean>>();
    for (final Patch p : patches) mipmapFutures.add(p.updateMipMaps());
    for (final Future<Boolean> f : mipmapFutures) f.get();
    Utils.log("Matching intensities done.");
}